Morrowind indeed has a pretty standard "save the world" story (but with a twist). Daggerfall had a much better main story, the entire intrigue unravelled slowly and there were people actively trying to screw your character over if at one point you chose to trust the wrong person.
And if your reputation with one of the factions was too low, you'd get assassins after your hide.
Biggest flaw, though, is multiple endings that in the end had no effect on the game world whatsoever because even in 1996 Bethesda realized that people would want to continue playing after the main quest. Remember all the clamour when your character "died" at the end of Fallout 3.